affyPLM 1.18.1
Ben Bolstad
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/affyPLM | | Last Changed Rev: 36979 / Revision: 38965 | | Last Changed Date: 2009-01-27 09:35:24 -0800 (Tue, 27 Jan 2009) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/affyPLM.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.18.1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affyPLM' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating affyPLM-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/cygdrive/e/biocbld/bbs-2.3-bioc/meat/affyPLM.Rcheck/tests'
Running 'C_code_tests.R'
Running 'PLM_tests.R'
Running 'preprocess_tests.R'
Running 'threestepPLM_tests.R'
make[1]: Leaving directory `/cygdrive/e/biocbld/bbs-2.3-bioc/meat/affyPLM.Rcheck/tests'
OK
* checking package vignettes in 'inst/doc' ... OK
* creating affyPLM-manual.tex ... OK
* checking affyPLM-manual.tex using pdflatex ... OK
installing R.css in E:/biocbld/bbs-2.3-bioc/meat/affyPLM.Rcheck
---------- Making package affyPLM ------------
adding build stamp to DESCRIPTION
making DLL ...
making LESN.d from LESN.c
making PLM_avg_log.d from PLM_avg_log.c
making PLM_biweight.d from PLM_biweight.c
making PLM_log_avg.d from PLM_log_avg.c
making PLM_medianPM.d from PLM_medianPM.c
making PLM_median_logPM.d from PLM_median_logPM.c
making PLM_medianpolish.d from PLM_medianpolish.c
making PLM_modelmatrix.d from PLM_modelmatrix.c
making SCAB.d from SCAB.c
making chipbackground.d from chipbackground.c
making common_types.d from common_types.c
making do_PLMrlm.d from do_PLMrlm.c
making do_PLMrma.d from do_PLMrma.c
making do_PLMthreestep.d from do_PLMthreestep.c
making idealmismatch.d from idealmismatch.c
making lm_threestep.d from lm_threestep.c
making matrix_functions.d from matrix_functions.c
making nthLargestPM.d from nthLargestPM.c
making preprocess.d from preprocess.c
making psi_fns.d from psi_fns.c
making qnorm_probeset.d from qnorm_probeset.c
making read_rmaexpress.d from read_rmaexpress.c
making rlm_PLM.d from rlm_PLM.c
making rlm_threestep.d from rlm_threestep.c
making rmaPLM_pseudo.d from rmaPLM_pseudo.c
making rma_PLM.d from rma_PLM.c
making rma_common.d from rma_common.c
making scaling.d from scaling.c
making threestep.d from threestep.c
making threestep_PLM.d from threestep_PLM.c
making threestep_common.d from threestep_common.c
making threestep_summary.d from threestep_summary.c
making threestep_summary_methods.d from threestep_summary_methods.c
making transfns.d from transfns.c
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c preprocess.c -o preprocess.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c:100: warning: 'rlmPLM_alloc_space' defined but not used
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60: warning: unused variable 'i'
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c threestep.c -o threestep.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -I"e:/biocbld/bbs-2.3-bioc/R/library/preprocessCore/include" -O3 -Wall -c transfns.c -o transfns.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include -i affyPLM_res.rc -o affyPLM_res.o
gcc -std=gnu99 -shared -s -o affyPLM.dll affyPLM.def LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o affyPLM_res.o -Le:/biocbld/bbs-2.3-bioc/R/bin -lgfortran -Le:/biocbld/bbs-2.3-bioc/R/bin -lRlapack -Le:/biocbld/bbs-2.3-bioc/R/bin -lRblas -lRzlib -lR
... DLL made
installing DLL
installing R files
installing inst files
preparing package affyPLM for lazy loading
Loading required package: affy
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: splines
Loading required package: preprocessCore
Creating a new generic function for "weights" in "affyPLM"
Creating a new generic function for "summary" in "affyPLM"
Creating a new generic function for "resid" in "affyPLM"
Creating a new generic function for "residuals" in "affyPLM"
installing man source files
installing indices
installing help
>>> Building/Updating help pages for package 'affyPLM'
Formats: text html latex example chm
Note: removing empty section \usage in file 'MAplot.Rd'
Note: removing empty section \usage in file 'MAplot.Rd'
MAplot text html latex chm
Note: removing empty section \examples in file 'PLMset-class.Rd'
Note: removing empty section \examples in file 'PLMset-class.Rd'
PLMset-class text html latex chm
PLMset2exprSet text html latex example chm
ReadRMAExpress text html latex chm
affyPLM-internal text html latex chm
bg.correct.LESN text html latex example chm
fitPLM text html latex example chm
normalize.exprSet text html latex example chm
normalize.quantiles.probeset text html latex chm
normalize.scaling text html latex example chm
preprocess text html latex example chm
Note: removing empty section \examples in file 'pseudo.Rd'
Note: removing empty section \examples in file 'pseudo.Rd'
pseudo text html latex chm
rmaPLM text html latex example chm
threestep text html latex example chm
threestepPLM text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\affyPLM.Rcheck\00_pkg_src\affyPLM\chm\affyPLM.chm
Compile time: 0 minutes, 0 seconds
16 Topics
111 Local links
3 Internet links
1 Graphic
Created e:\biocbld\bbs-2.3-bioc\meat\affyPLM.Rcheck\00_pkg_src\affyPLM\chm\affyPLM.chm, 39,622 bytes
Compression decreased file by 54,704 bytes.
adding MD5 sums
* DONE (affyPLM)